If you have a lot of things starting up, that can slow down your computer. Even mine is fairly slow the first few minutes because of these things, mostly Dropbox actually. I've noticed it being a major CPU hog while starting up.
You can download
Microsoft's Autoruns and use it to disable certain startup programs and modules. If there are things you don't need, disable them. That's what I do. For example I disabled Google Updater Service from starting up because if a Google product needs updating, it will probably tell me at least 15 times before I start the application anyway.
I'm unsure about the Skype issue though. I know Skype is absolutely awful, but I haven't really experienced that particular issue with it.